Submissions for variant NM_025152.3(NUBPL):c.815-27T>C

gnomAD frequency: 0.00348  dbSNP: rs118161496

Total submissions: 13

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000198391	SCV000251972	pathogenic	not provided	2017-08-14	criteria provided, single submitter	clinical testing	Expression studies of the c.815-27 T>C sequence change found that this variant impairs mRNA splicing resulting in a 80% decrease in complex I assembly and function (Tucker et al., 2012; Wydro et al., 2013). Therefore, based on the currently available information, the c.815-27 T>C variant is a strong candidate for a pathogenic variant; however, the possibility that it is a benign variant cannot be excluded.
Ambry Genetics	RCV000210589	SCV000262906	likely pathogenic	Inborn genetic diseases	2021-04-13	criteria provided, single submitter	clinical testing	The c.815-27T>C intronic alteration consists of a T to C substitution 27 nucleotides before coding exon 10 in the NUBPL gene and is predicted to affect the native branch site. Based on data from the Genome Aggregation Database (gnomAD) database, the NUBPL c.815-27T>C alteration was observed in 0.35% (992/280082) of total alleles studied (including 10 homozygotes), with a frequency of 1.24% (310/24978) in the European (Finnish) subpopulation. The [c.166G>A (p.G56R); c.815-27T>C] complex allele has been reported in the homozygous state, compound heterozygous state, and confirmed in trans with a second pathogenic allele in multiple unrelated patients with mitochondrial encephalomyopathy (Calvo, 2010; Kevelam, 2013). Emerging evidence is suggestive that the NUBPL [c.166G>A (p.G56R); c.815-27T>C] complex allele is likely pathogenic when these alterations are in cis; however, the clinical significance of these alterations in isolation remains uncertain. The c.815-27T nucleotide is highly conserved in available vertebrate species. Functional analysis of cultured fibroblasts from a patient bearing the [c.166G>A (p.G56R); c.815-27T>C] complex allele in trans with a complex rearrangement, as well as a control patient who was heterozygous for only the c.815-27T>C alteration, demonstrated an aberrant RT-PCR pattern with three distinct transcripts: wild-type, a lengthened transcript resulting from a cryptic splice site which introduces an additional 72 bp and results in a frameshift (p.G272Vfs*11), as well as a truncated transcript generated due to exon 10 skipping resulting in a frameshift (p.D273Qfs*31) (Tucker, 2012). Analysis by qRT-PCR and Western blot showed that the heterozygous control with only the c.815-27T>C alteration had reduced mRNA expression (74%) and protein expression (59%) compared to wild type controls, and the patient with the [c.166G>A (p.G56R); c.815-27T>C] complex allele and complex rearrangement on the other allele had more significant reduction in mRNA expression (15%) and undetectable protein expression (Tucker, 2012). No defective function was identified when the protein with the G56R missense change was over-expressed (Tucker, 2012). The p.D273Qfs*31 transcript is completely non-functional in yeast assays (Wydro, 2013; Maclean, 2018). In silico splice site analysis predicts that the c.815-27T>C alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. Based on the available evidence, this alteration is classified as likely pathogenic.
CeGaT Center for Human Genetics Tuebingen	RCV000198391	SCV000493198	uncertain significance	not provided	2023-02-01	criteria provided, single submitter	clinical testing	NUBPL: PM3:Strong, PS3:Moderate, PM2:Supporting, PP3, BS2
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	RCV000198391	SCV000511195	uncertain significance	not provided	2017-01-09	criteria provided, single submitter	clinical testing	Converted during submission to Uncertain significance.
Mayo Clinic Laboratories, Mayo Clinic	RCV000660543	SCV000782648	likely pathogenic	Mitochondrial complex I deficiency	2017-05-01	criteria provided, single submitter	clinical testing
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital	RCV001249675	SCV001423626	likely pathogenic	Mitochondrial complex 1 deficiency, nuclear type 21	2018-06-15	criteria provided, single submitter	clinical testing	[ACMG/AMP: PS3, PP3, PP5, BS1] This alteration is supported by well-established in vitro or in vivo functional studies to have a damaging effect on protein function or splicing [PS3], is predicted to be damaging by multiple functional prediction tools [PP3], was reported as a pathogenic/likely pathogenic alteration by a reputable source (ClinVar or other correspondence from a clinical testing laboratory) [PP5], has an allele frequency that is greater than expected for the associated disease [BS1].
Undiagnosed Diseases Network, NIH	RCV001249675	SCV001736867	uncertain significance	Mitochondrial complex 1 deficiency, nuclear type 21	2020-08-24	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV001249675	SCV002511894	pathogenic	Mitochondrial complex 1 deficiency, nuclear type 21	2023-07-07	criteria provided, single submitter	clinical testing	Variant summary: NUBPL c.815-27T>C is located at a position not widely known to affect splicing. 4/4 computational tools predict no significant impact on normal splicing. However, at least two publications report experimental evidence that this variant affects mRNA splicing (Tucker_2012, Kimonis_2021). The variant allele was found at a frequency of 0.0034 in 248676 control chromosomes in the gnomAD database, including 10 homozygotes. c.815-27T>C has been reported in the literature in multiple individuals affected with Mitochondrial Complex 1 Deficiency, Nuclear Type 21 (Calvo_2010, Kevelam_2013, Kimonis_2021), and some were reported as compound heterozygous with other (likely) pathogenic variants. These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein expression, finding that a heterozygous control with the variant exhibited far lower expression of NUBPL protein (Tucker_2012). The following publications have been ascertained in the context of this evaluation (PMID: 20818383, 23553477, 22072591, 32518176). 11 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, and classified it as pathogenic/likely pathogenic (n=8) or uncertain significance (n=3). Based on the evidence outlined above, the variant was classified as pathogenic.
Mendelics	RCV001249675	SCV002517825	pathogenic	Mitochondrial complex 1 deficiency, nuclear type 21	2022-05-04	criteria provided, single submitter	clinical testing
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV001249675	SCV002768840	uncertain significance	Mitochondrial complex 1 deficiency, nuclear type 21	2020-10-19	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as 3B-VUS. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0106 - This gene is known to be associated with autosomal recessive disease. (N) 0210 - Splice site variant (canonical or non-canonical) proven to affect splicing/expression of the transcript with a known effect on protein structure. Functional studies showed three alternate transcripts were generated as a result of aberrant splicing from the allele with this variant: one transcript with normal splicing, one with exon 10 skipped resulting in a frameshift but no nonsense-mediated decay (NMD), and a third transcript that utilised a cryptic splice site resulting in a frameshift and NMD (PMIDs: 22072591, 32518176). (P) 0251 - Variant is heterozygous. (N) 0305 - Variant is present in gnomAD >=0.01 and <0.03 for a recessive condition (972 heterozygotes, 10 homozygotes). (N) 0705 - No comparable variants have previous evidence for pathogenicity. (N) 0803 - Low previous evidence of pathogenicity in unrelated individuals. An allele harbouring this variant in cis with a second variant (p.(Gly56Arg)) has been reported as pathogenic in many patients, majority of whom were in compound heterozygous state with a pathogenic allele (PMIDs: 22072591, 25245479, 23553477). However, an allele harbouring this variant without the p.(Gly56Arg) variant has been associated with disease in one family (PMID: 32518176). (P) 1001 - Strong functional evidence supporting abnormal protein function. Functional studies showed levels of NUBPL mRNA and protein were decreased in the fibroblast cells heterozygous for this variant alone (PMID: 22072591). (P) 1205 - Variant is maternally inherited. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign
Revvity Omics, Revvity	RCV001249675	SCV003810621	likely pathogenic	Mitochondrial complex 1 deficiency, nuclear type 21	2024-01-08	criteria provided, single submitter	clinical testing
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000660543	SCV004847434	uncertain significance	Mitochondrial complex I deficiency	2024-02-16	criteria provided, single submitter	clinical testing	The c.815-27T>C variant in NUBPL is typically observed as a compound allele (in cis) with the c.166G>A [p.G56R] variant in individuals with mitochondrial complex I deficiency. By itself, it has been reported in at least one individual with mitochondrial complex I deficiency and an another variant in trans, and segregated with disease in at least 1 sibling (Kimonis 2021 PMID: 32518176; Maclean 2018 PMID:29982452). This variant has also been identified in 1.28% (819/63974) of European (Finnish) chromosomes, including 22 homozygotes, by gnomAD (http://gnomad.broadinstitute.org, v4.0.0) and reported in ClinVar (Variation ID 50317). This variant is located in the splice branch site, and computational prediction tools suggest an impact on splicing. An RT-PCR study demonstrated that this variant results in three transcripts: wild-type, the use of a cryptic acceptor site (p.G272VfsX11), or skipping of exon 10 (p.D273QfsX31). In addition, in vitro functional studies demonstrated that patient cells express reduced levels of the wild-type transcript, possibly as a result of degradation of a variant transcript by NMD (Tucker 2012 PMID: 22072591). Overall, it is unclear if this variant in isolation causes disease or whether it acts in synergy with the p.G56R variant. Therefore, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PM3, PP1, PP3, PS3_Supporting, BS1_Supporting.
OMIM	RCV001249675	SCV001759967	pathogenic	Mitochondrial complex 1 deficiency, nuclear type 21	2021-07-20	no assertion criteria provided	literature only